• Dataset: MiRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus and associations with survival.

  • Cancerous and noncancerous tissues.
  • Cancer stages.
  • 100 ADC and 70 SCC patients.
  • North American and Japanese cohorts.
  • Other variables (tabacco, alcohol)

• Objective of the project: To reproduce the findings of the authors and elaborate on their visualizations.

Patient data:

• GSE13937_series_matrix.txt
  

• National Center for Biotechnology Information website (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13937)

Microarray information:

• A-GEOD-8835.adf.txt and A-GEOD-8835_comments.txt

• European Bioinformatics Institute website (https://www.ebi.ac.uk/arrayexpress/arrays/A-GEOD-8835/)

• Data quality: absence of the different North American cohorts hindered the reproducibility of the article.

-Data wrangling: complex data set which required decision-making regarding the selection of relevant probes, NA values, and others.

• Survival:

• Differential expression: we weren’t able to reproduce the results, but we found more differentially expressed miRNAs.

• Principal Component Analysis: